Pouille, who won in Montpellier and lost in the final of Marseille in the past three weeks, will take on third-seeded Roberto Bautista Agut, who ended the dream run of Tunisian wild card Malek Jaziri 6-3, 6-4.
Unseasonal rain in Dubai delayed the start of the Pouille-Krajinovic semi for half an hour. Later, there was a seven-minute interruption at 5-5 in the second set, and a 30-minute stoppage when Pouille led 4-3 in the third.
The second-seeded Pouille, expected to rise in the rankings from 15 to the top 10 if he wins on Saturday, wrapped up the first set with his sixth ace.
The Dubai resident, a semifinalist last year, beat Krajinovic in the Marseille quarterfinals last week. Just when it looked like a much easier outing this time as he led by 4-2 and a break in the second set under a light drizzle, Pouille's solid serve started faltering and his unforced errors began rising.
Krajinovic took advantage and took the set. The decider went with serve and Pouille prevailed in another tiebreaker after more than two hours.
"A loss would have hurt a lot," Pouille said. "I was much better in the first and second set, 6-3, 5-3. I made a mistake to continue playing when it was raining. After that we couldn't even move. It was just serve and return.
"In the third, it was very, very close. I'm just very happy I got through."
Jaziri, ranked 117th, ousted top-seeded Grigor Dimitrov in the opening round but couldn't match Bautista Agut.
Bautista Agut broke serve in the second game for the first set, and even though Jaziri gave a better fight in the second with a break of his own, the Spaniard converted both of his break chances to reach his 14th career final. He won his seventh career title in January in Auckland.